Phylogeography And Landscape Genomics Of Chinese Lacquer Tree (Toxicodendron Vernicifluum, Anacardiaceae)

Toxicodendron vernicifluum(Stokes)F.A.Barkley is a deciduous tree species in the sumac family Anacardiaceae.It is commonly known as Chinese lacquer tree,which can provide us with raw lacquer,an excellent adhesive and painting material.The species is also used for producing timber and traditional medicine and has been cultivated in East Asia for probably thousands of years.In the past decade,the research on Chinese lacquer trees has mainly focused on secondary metabolites,anatomic features,and growth traits.Although previous studies have described the genetic variation patterns of local populations of the species in China,South Korea,and Japan,the information on the overall genetic structure was still limited by a narrow sampling range and small sample size.In this study,we collected samples throughout the natural distribution of the species and used both chloroplast(cp)DNA and nuclear single nucleotide polymorphisms(SNPs)to elucidate the genetic variation pattern of natural T.vernicifluum populations.We applied multiple methods of phylogeography,population genetics,landscape genetics,phylogenetics,and ecological niche modeling(ENM)to(1)evaluate the effects of topography and climate on the genetic variation patterns of T.vernicifluum;(2)infer the lineage divergence and demographic history of T.vernicifluum;(3)identify SNPs significantly associated with environmental variables and predict the genetic vulnerability of natural populations under future climate warming scenarios.The main findings and conclusions of this study are as follows:(1)We sequenced,assembled,and annotated the complete cp genomes of six individuals of T.vernicifluum,one individual of T.succedaneum,and one individual of T.sylvestre.Each of the eight cp genomes encoded 87 protein-coding genes,37 t RNA genes,and eight r RNA genes.Phylogenetic analyses based on protein-coding genes indicated that T.vernicifluum individuals from western China formed a monophyletic group sister to the cluster containing those from eastern China.The cp genomes of T.vernicifluum from western China exhibited a larger genome size and longer large single-copy(LSC),small single-copy(SSC),and inverted repeat(IR)regions than those from eastern China.A total of 466 SNPs and 141 indels were detected among the cp genomes of T.vernicifluum,most of which were found between the eastern and western lineages.The two groups exhibited a similar number of microsatellites,long repeats,and tandem repeats.Notably,complementary repeat sequences were only found in the individuals of eastern China while reverse repeats were only detected in the individuals from western China.N umerous mutational hotspots(e.g.,trn F-ndh J,rpl32-trn L,ccs A-ndh D,trn H-psb A,psb C-trn S,trn L-trn F,rpl32,and rps19)were also identified which can be used as potential molecular markers in phylogeographic studies of T.vernicifluum.(2)We assessed the range-wide genetic variation of 79 T.vernicifluum populations(449individuals)sampled from China,South Korea,and Japan using two cp DNA sequences(trn L and trn L-F).A total of five chloroplast haplotypes were identified based on seven substitutions across the 717-bp alignment.A clear east-west phylogeographic break was recovered according to the three-step landforms of mainland China.The wild trees of the western clade were found to be geographically restricted to the middle step‘,which is characterized by high mountains and plateaus,e.g.,the Yunnan-Guizhou Plateau,the Qinling Mountains,the Daba Mountains,and the Taihang Mountains;while those of the eastern clade were confined to the low step‘ of mainland China,the Korean Peninsula,and Japan.This break was much sharper than previously reported and was found to occur at a much larger scale,extending from subtropical(e.g.,the Xuefeng Mountain)to warm-temperate China(e.g.,the Taihang Mountain).Our results suggested that the cool glacial climate may have caused the ancestral population of T.vernicifluum to retreat to at least two glacial refugia,leading to allopatric divergence in response to long-term geographic isolation.Migration vector analyses based on the outputs of ENMs supported a gradual range expansion of T.vernicifluum since the LIG.Mountain ranges in western China and the East China Sea land bridge were inferred to be dispersal corridors in the western and eastern distributions of T.vernicifluum,respectively.Combining the evidence from fossil records and molecular analyses,we inferred that the T.vernicifluum trees in Japan may have a natural origin in eastern China.(3)We investigated the phylogeographic structure of 39 T.vernicifluum populations(357individuals)sampled from both western and eastern China using four cp DNA sequences(trn L,trn L-F,trn H-psb A,and mat K).A total of 19 haplotypes were identified based on 22 substitutions,five indels,and one inversion event.The median-joining network grouped the haplotypes into eastern and western clades,which were estimated to have diverged during the Late Pliocene to Early Pleistocene(2.38 Ma;95% HPD: 1.45–3.68 Ma).The divergence between those two clades was probably associated with the recent uplift of the Qinghai-Tibetan Plateau(QTP)and the intensification of the East Asian summer monsoon.Within the western clade,we identified three groups of private haplotypes,i.e.,the haplotypes private to the N ujiang population(NUJ),Yunnan Province;the haplotypes private to the Guizhou Plateau and Wuling Mountains;and the haplotypes private to the Q inling-Daba Mountains.The niche identity test also showed that the level of climate niche overlapping was low between the latter two groups of private haplotypes,suggesting that weak north-south differentiation may have occurred among T.vernicifluum populations in western China.Genetic barrier analyses supported that eastern China,the Qinling-Daba Mountains,the Guizhou Plateau,and Yunnan Nujiang are priority conservation units of T.vernicifluum.Some populations at the distribution edge,e.g.,Huangshan,Anhui(AHH)and Jiaokou,Shanxi(JIK)also showed obvious genetic differentiation with adjacent populations,which can also be used as independent protection units.Significant genetic boundaries were also detected among adjacent populations in the Guizhou Plateau and Wuling Mountains,e.g.,Zigui,Hubei(MPX);Chishui,Guizhou(CHI);Leigongshan,Guizhou(LGS);Yunshan,Hunan(YUN);and Baojing,Hunan(BYS).Attention should be paid to protecting the genetic uniqueness of T.vernicifluum populations in this region.(4)We used specific locus amplified fragment sequencing(SLAF-seq)to obtain nuclear SNP information for 39 T.vernicifluum populations(175 individuals)in China.An average of5,697,771 clean reads were generated for each individual,with a mean mapping rate of 85.47%.Principal component analysis(PCA),ADMIXTURE analysis,and phylogenetic analysis indicated that the T.vernicifluum populations could be divided into eight genetic groups: N ujiang in Yunnan(NUJ),the Guizhou Plateau(GZP),the Q inling-Daba Mountains 1(QB1),the Taihang Mountains(THS),eastern China(EAS),the Qinling-Daba Mountains 2(QB2),the Xingdoushan Mountains in Hubei(XDS),and Zigui in Hubei(MPX).Among those,the former five genetic groups were found to be dominated by a single genetic cluster,while the latter three genetic groups showed an admixture of two different genetic clusters.Demographic history simulations indicated that the eastern China and western China clades may have diverged during the Late Pliocene to Early Pleistocene(2.66 Ma;95% CI: 1.95-3.96 Ma).These analyses also supported the XDS group may have originated through a genetic admixture event between GZP and EAS groups.Latent factor model(LFMM)analyses revealed that 205 SNPs were significantly associated with environmental variables,of which most were related to altitude and temperature factors.Gradient Forest(GF)analysis showed that altitude,isothermality,temperature seasonality,and precipitation of the wettest month have high explanatory power for the adaptive genetic variation pattern of wild T.vernicifluum trees.The populations in eastern and southern China have higher reverse genetic offsets under future climate warming scenarios.Specifically,the populations in eastern China,the Yunnan-Guizhou Plateau,and the Xingdoushan Mountains may be more genetically vulnerable to climate change.Overall,our study provided evidence from both chloroplast and nuclear genomes to support the occurrence of two major lineages of T.vernicifluum: eastern China and western China.Those two groups can be divided according to the boundary between the middle step‘ and low step‘ of the stepped landforms of mainland China.In western China,T.vernicifluum populations also exhibited genetic differentiation among regions such as Nujiang in Yunnan,the Guizhou Plateau,the Q inling-Daba Mountains,and the Taihang Mountains.Furthermore,wild T.vernicifluum trees in the Daba and Wuling Mountains may have originated through the genetic admixture between the eastern and western lineages.Our results indicated that T.vernicifluum populations in eastern China,the Yunnan-Guizhou Plateau,and the Xingdoushan Mountains are more vulnerable to the threat of rapid climate change in the future.